Sequence
atgc intronic sequence ATGC exonic sequencegtaagagtttaaatctatctatcgagtacacatttatatttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 26 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
------------------------------------gtaagagtttaaatctatctatcgagtacacatttatatttccccttaaat-actaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
| | | | || | | || ||| || | | |||| | | ||| | | || | | | || ||||||| || || | | || ||||| | | ||||| || || || ||||| ||||| || ||||||||||| |||||| | |||||||||||||
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatt------tctggagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
----------------------gtaagagtttaaatctatctatcgagtacacatttatatttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
|| || | | || | | |||| || | || | | | ||| | | | | | | || | ||||| || || | |||| ||||| | | ||||| || || || ||||| ||||| || ||||||||||| |||||| | |||||||||||||
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatt--tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
gtaagagtttaaatctatctatcgagtacac-atttat--atttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
| | || || || || || |||| | || | | || || || |||| || | ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || |||||||||||||| || ||||| ||||||||||| ||||
---gttggctgcattcattcttcatgttgactatttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 26
--gtaagagtttaaatctatctatcgagtacacatttatatttcccctt---aaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
|| | ||| || | || | | ||| | ||| | |||| | |||| ||| | || || ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || ||||| |||||||| || ||||||||||||||||| ||||
gtgtggaaatttg---ctcttaattggaactatttttttgttttagttgtggaaatctcagattattactatt--actgtatgatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
gtaagagtttaaatctatctatcgagtacac-atttatatttcccctta---aatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
|| || | || ||| || || || |||| | | | ||| | || | | || |||| ||| | ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || ||||||||||| || || ||||| ||||||||||||||||
gttag---ctgcatttattcttcatgttgactatttttcagttcaattataggaaaccagtggattattattatttggaatg---cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
--gtaagagtttaaatctatctatcgagtacacatttatatttcccctt---aaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
|| | ||| || | || | | ||| |||| || |||| | |||| ||||| | || ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || ||||| |||||||| || ||||||||||||||||| ||||
gtgtggaaatttg---ctcttaattggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacg---cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 26
--gtaagagtttaaatctatctatcgagtacacatttatatttcccctt---aaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
|| | ||| || | || | | ||| |||| || |||| | |||| ||||| | || ||||||| || || |||||| |||| ||||||||||| ||||||||||| || |||||
gtgtggaaatttg---ctcttaattggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacg---cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAG-------------------------------------------
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
gtaagagtttaaatctatctatcgagtacacatttatatttccccttaaatactaatttat---------cgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
|| |||| ||| | | | ||| | | | || ||| || || | | ||| ||| | |||||||||||||||||||| |||| ||||||||||| ||||||||||| || |||||||| || |||||||||||||| ||||| ||||| |||||||| |
gtg-gagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116461287|gb|EG503879.1|EG503879EST: AGTCTATTGATTTGCATGACAGTTTTGACCAGATAGGTCTCGCTCAGAAG ATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTAT
genomic: AGTCTATTGATTTGCATGACAGTTTTGACCAGATAGGTCTCGCTCAGAAGgtaagagttt ... tgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttatatttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
tactaat putative branch site (score: 1)
ttaaatactaatttat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagtttaaatctatctatcgagtacacatttatatttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA